Thursday, December 25, 2014

By mimicking the red and green colors of
falling leaves, Bornean lizards avoid falling prey to birds whilst gliding, new
research has found. The work suggests that populations of the gliding lizard, Draco
cornutus, have evolved extendable gliding membranes, like wings, which
closely match the colors of falling leaves to disguise themselves as they glide
between trees in the rainforest.

Found throughout
South-East Asia, Draco is the only living genus of lizard with extendable
gliding membranes -- call patagia -- which allow them to glide between trees in
their territories.

Published Dec. 24 in
the international journal Biology Letters, the study was conducted
by PhD student Ms Danielle Klomp, based at both the University of Melbourne and
the University of New South Wales with supervisors Dr Terry Ord and Dr Devi
Stuart-Fox and collaborator Dr Indraneil Das from the University of Malaysia.

The team travelled to
Borneo and observed two populations of a gliding lizard that have different colored
gliding membranes and occupy very different habitats.

One population has red
gliding membranes, which match the color of the red falling leaves of their
coastal mangrove forest habitat. The other population has dark brown and green
gliding membranes, which match the colors of falling leaves in their lowland
rainforest habitat.

They determined how
the colors would be perceived by a predatory bird and found that the gliding
membrane color would be indistinguishable from a falling leaf in the same
forest.

Birds can see
ultraviolet light as well as the colors that humans see, so it is important to
take into account how closely the colors would actually match to a bird, Ms
Klomp said.

"It's a cool
finding because these gliding lizards are matching the colors of falling leaves
and not the leaves that are still attached to the tree. In the mangrove
population the leaves on the trees are bright green, but turn red shortly
before falling to the ground, and it is this red color that the lizards mimic
in their gliding membranes. This allows them to mimic a moving part of the
environment- falling leaves -- when they are gliding." Ms Klomp said.

Because some animals
have developed color not only for camouflage, but also as a form of
communication, we also wanted to watch the lizards interact in the wild and
determine whether their gliding membranes were used for communication as well
as gliding said Ms Klomp.

The team filmed hours
of gliding lizard behavior to observe how often the colors were displayed to
other lizards.

"We found that
both the red and green/brown gliding membranes seem to have evolved to
specifically resemble the falling leaves in each population's particular
habitat, and are rarely used for communication," Ms Klomp said.

"Perhaps these
populations may have originally had the same gliding membrane colors but as
they have moved into different forest types their colors have adapted to
closely resemble the colors of falling leaves in the different forests, known
as divergent evolution."

Thursday, December 11, 2014

Note:
It is the end of the year and this blog is going to be in hibernation for a
short time. So this post may be the last for several weeks. But it will be
active again in the near future.

Species that forage exclusively at the sea’s
surface but spend much of the rest of their time submerged could offer a rare
opportunity to shed light on the evolution of diving behavior that is
independent from foraging. The viviparous Yellow-bellied Sea Snake, Hydrophis (formerly Pelamis) platurus
(Hydrophiinae), also known as the Pelagic Sea Snake, provides this opportunity.

In a recent paper in Animal Behaviour, Cook
and Brischoux (2014) note the Pelagic Sea Snake drifts passively with surface
and subsurface currents, spending its entire life cycle at sea. The result is a
wide distribution covering the entire tropical Indo-Pacific basin, one of the
largest distributions of any squamate reptile. Another remarkable feature of the
Pelagic Sea Snake’s unusual life history, is it spends most of its day-to-day
life floating in the water column 20 to 50 m deep. Submergence time is
interrupted by surfacing, which can be brief to breathe or longer to forage.
The foraging strategy of the Pelagic Sea Snake is remarkable for a marine
tetrapod, it ambushes larval fish that are concentrated under debris on oceanic
labile features such as slicks or drift lines, doing ‘float-and-wait’ foraging
at the oceanic surface.

Hydrophis
platurus
is the only marine tetrapod foraging specifically at the ocean surface, but spending
a considerable proportion of its time budget submerged. An activity pattern
offering a unique opportunity to study diving independently from foraging.

The authors found the Pelagic Sea Snake
spends 95% of its time underwater, where it can dive to 50 m and stay for 3.5 hours
without breathing. Dives are S-shaped, with a long phase of gradual ascent
during which the snake is neutrally buoyant. Snake lungs deflate slowly during
this phase at a rate that increases with water temperature, and thus
metabolism. Dive duration is linked to inferred lung volume at the start of the
dive, suggesting aerobic diving.

The pelagic sea snakes dive for multiple
reasons, but the primary reason seems to be to avoid sea surface turbulence.
Underwater, they can reduce metabolism by targeting cooler water layers. And by
hovering in the water column, they reduce energy expenditure and escape both
surface and bottom predators. At the same time they can more easily locating
their own prey from underneath.

A detailed analysis of the diving behavior
of H. platurus shows how this exclusively marine species of tetrapod manages
its dive cycle and the influence environmental parameters have upon its diving
and surfacing behaviors. This has opened the door to a better understanding of
the adaptations developed by this species.

Interestingly, there is an important
parallel in behavior between H. platurus and several species of marine turtles.
Adaptations in both these lineages of reptiles reflect a response to pressures
of the marine environment experienced during the evolutionary transition from
terrestrial to oceanic life. Unfortunately, the behavior of sea snakes at sea
is still inadequately known compared to that of marine turtles despite being a
highly diversified group comprising four families and ca. 90 species.

The authors suggest the study of sea
snakes can help interpret diving behavior in other lineages of marine reptiles.

Animals that regulate their body temperature through the external
environment may be resilient to some climate change but not keep pace with
rapid change, leading to potentially disastrous outcomes for biodiversity.

A study by the University of Sydney and University of Queensland showed
many animals can modify the function of their cells and organs to compensate
for changes in the climate and have done so in the past, but the researchers
warn that the current rate of climate change will outpace animals' capacity for
compensation (or acclimation).

The research has just been published in Nature Climate Change (Letters),
written by Professor Frank Seebacher School of Biological Sciences and
Professor Craig Franklin and Associate Professor Craig White from the
University of Queensland.

Adapting to climate change will not just require animals to cope with
higher temperatures. The predicted increase to fluctuations in temperature as
well as to overall temperature would require animals to function across a
broader range of conditions. This is particularly important for ectotherms,
animals that rely on external sources of heat to control body temperature, and
are therefore more influenced by environmental temperatures.

The research showed that many groups of ectotherms, which make up more
than 90 percent of all animals, are able to change their physiological function
to cope with an altered environment, but the rapid pace and fluctuations of
human-induced climate change present serious challenges.

The researchers studied 40 years of published data to assess how
biological functions change in response to a sudden fluctuations in environmental
temperatures. They found that the physiological rates of ectothermic animals,
such as heart rate, metabolism and locomotion, had already increased over the
past 20 years with increasing average temperatures.

"It is important that animals maintain the right balance between
the large number of physiological functions despite environmental fluctuations.
An increase in temperature that leads to changed reaction rates can upset that
balance and cause the decline of individuals and species," said Professor
Seebacher. "For example, movement requires energy and oxygen to be
delivered to muscles. However, if metabolism or the cardiovascular system can't
cope with increased temperatures, animals can no longer move to forage, migrate
or interact with each other.

"The overall trend in the last 20 years has been to increased
physiological rates, and we predict that this would continue to increase with
increasing temperature. "Even if animals are able to maintain the balance
of their physiological functions in a warmer climate, increased metabolism
leads to increases in the food resources needed and could upset the balance in
ecosystems, particularly if predator and prey populations respond very
differently to the environmental temperature change."

Tuesday, December 9, 2014

The Reptile Database (RDB)
is a very useful tool for herpetologists, and they released a new version a few
days ago. The new version lists 10,119
species (including 139 described this year), up from 10,038 in August, 35,615 references (including
1,203 published this year), up from 34,104 in August, which resulted in almost 200 new and changed names.

The site also is importing references for all of the papers published in Herpetology Notes and BioGecko, and they have about a 1000
papers from Sauria now crossed
reference and they can be individually ordered from the RBD.

The RDB Newsletter also noted some selected taxonomic news:

Homalopsidae: Murphy and
Voris (2014) suggested a number of new genera and revalidated a few more,
leading to 28 genera for just 53 species.

Boidae: Pyron et al. 2014
suggested to split the monophyletic boas into multiple families; we did not
follow this suggestion following a discussion with the Scientific Advisory
Board (see below). However, the new suggested families (such as “Sanziniidae)
can be found in the database.

The RDB recently constituted
a Scientific Advisory Board (SAB) to make general strategic decisions as well a
decisions on controversial taxonomic issues. One of the first recommendations
of the SAB was not to adopt the suggested Boid taxonomy suggested by Pyron et al. (2014, see above). We continue to
consult individual experts in more special cases, e.g. on individual species or
genera. There is a consensus that all published taxonomic changes should be in
the Reptile Database but when it comes to valid names they can only show one
“accepted” name for any given species even if several are in use. Instead of
flip-flopping between names with each new publication, the result will be a bit
more conservative but also more stable. The members of the SAB are listed on a
new page at http://www.reptile-database.org/db-info/sab.html.

Some new snake species described in 2014

In order to manage
data curation and data import better, we have started to recruit editors for
special tasks.

Paul Freed and Sven
Mecke are our first volunteer photo editors. They will receive the photos sent
to the RDB, edit them, verify correct identifications with experts, find photos
of species not pictured etc. This will also allow us to process photos faster. Thed
RBD is looking for a photo editor taking care of turtles.

Similar to the photo
editors, RBD is looking for volunteers willing to help with the curation of
papers. Initially we will start with editors for turtles, crocodiles, and
squamate families (or genera if they have a substantial number of species). The
taxonomic editors will receive papers from which they are supposed to extract
information that is relevant for the database such as taxonomic or
nomenclatural changes, new distribution records, or databasable life history
data.

The RBD is asking instructors teaching herpetology or taxonomy to help improve data curation by using it in their
classes. Students could curate papers, edit Wikipedia pages link to the Reptile
Database, ID species, or find and analyze other information. There is always a
large backlog of papers that need to be curated, including simple cases with
new distribution data or more complicated ones. Please get in touch if you are
interested. They have designed a few exercised and assignment for classroom
use: http://www.reptile-database.org/db-info/teaching.html.

RDB has a large number of new
photos (>1,500). However, these are added to the database independently of
text, and thus have not been updated yet. This will probably take another few
weeks or so, just in case you do not see the photos that you have submitted. In
any case, more photos are always welcome! Please send photos (with location or
coordinates) to info@reptile-database.org.

The RDB often use
Google Maps to verify the localities reported in papers. However, Google Maps
shows different maps in different countries. For instance, Google Maps in India
shows Arunachal Pradesh as part of India. However, Google Maps in China shows
Arunachal Pradesh as part of China. The RDB will replace current approximate
maps with “real" distribution maps sooner or later, such details are
important when you search the Reptile Database for geographic areas (or if you
need a list of all Indian or Chinese reptiles). Right now, they treat Arunachal
Pradesh as part of India. Finally, there are different names in different
Google Maps versions. For instance, in the international version you can see
the “Persian Gulf”. However, in Arabian countries it is called the “Arabian
Gulf”. There are a number of other contentious borders or names, so please keep
this in mind when you search the database.

In the course of
history new countries form, such as the new countries that used to be
Yugoslavia or North and South Sudan (which used to be Sudan). However, there
are also new states, such as the new state of Telangana in India, and the
Indian government apparently discusses the creation of another 21 new states
(the current states are fairly new too, many formed in 1956). Obviously, this
can cause headaches in trying to keep tabs on reptiles in those states,
especially when they are species-rich such as those in India. Please let RDB
know if you see discrepancies or errors.

A new web service and
database, http://journalmap.org/ offers a
scientific literature search engine that empowers you to find
relevant research based on location and biophysical attributes combined
with traditional keyword searches. Give it a try.

The RDBdoes not have funding.
If you plan to submit a grant related to reptile taxonomy or with databasable
information, they are asking members to consider including the Reptile Database
as a subcontractor or collaborator. Or budget personnel to curate data for the
RDB.

Monday, December 8, 2014

Technology that can map
out the genes at work in a snake or lizard's mouth has, in many cases, changed
the way scientists define an animal as venomous. If oral glands show expression
of some of the 20 gene families associated with "venom toxins," that
species gets the venomous label.

But, a new study from
The University of Texas at Arlington challenges that practice, while
also developing a new model for how snake venoms came to be. The work, which is
being published in the journal Molecular Biology and Evolution, is
based on a painstaking analysis comparing groups of related genes or "gene
families" in tissue from different parts of the Burmese python, or Python
molurus bivittatus.

A team led by assistant
professor of biology Todd Castoe and including researchers from Colorado and
the United Kingdom found similar levels of these so-called toxic gene families
in python oral glands and in tissue from the python brain, liver, stomach and
several other organs. Scientists say those findings demonstrate much about the
functions of venom genes before they evolved into venoms. It also shows that
just the expression of genes related to venom toxins in oral glands of snakes
and lizards isn't enough information to close the book on whether something is
venomous.

"Research on venom
is widespread because of its obvious importance to treating and understanding
snakebite, as well as the potential of venoms to be used as drugs, but, up
until now, everything was focused in the venom gland, where venom is produced
before it is injected," Castoe said. "There was no examination of
what's happening in other parts of the snake's body. This is the first study to
have used the genome to look at the rest of that picture."

Learning more about
venom evolution could help scientists develop better anti-venoms and contribute
to knowledge about gene evolution in humans

Castoe said that with
an uptick in genetic analysis capabilities, scientists are finding more
evidence for a long-held theory. That theory says highly toxic venom proteins
were evolutionarily "born" from non-toxic genes, which have other
ordinary jobs around the body, such as regulation of cellular functions or digestion
of food.

"These results
demonstrate that genes or transcripts which were previously interpreted as
'toxin genes' are instead most likely housekeeping genes, involved in the more
mundane maintenance of normal metabolism of many tissues," said Stephen
Mackessy, a co-author on the study and biology professor at the University of
Northern Colorado. "Our results also suggest that instead of a single
ancient origin, venom and venom-delivery systems most likely evolved
independently in several distinct lineages of reptiles."

Castoe was lead author
on a 2013 study that mapped the genome of the Burmese python. Pythons are not
considered venomous even though they have some of the same genes that have
evolved into very toxic venoms in other species. The difference is, in highly venomous
snakes, such as rattlesnakes or cobras, the venom gene families have expanded
to make many copies of those shared genes, and some of these copies have
evolved into genes that produce highly toxic venom proteins.

"The non-venomous
python diverged from the snake evolutionary tree prior to this massive
expansion and re-working of venom gene families. Therefore, the python
represents a window into what a snake looked like before venom evolved,"
Castoe said. "Studying it helps to paint a picture of how these
gene families present in many vertebrates, including humans, evolved into
deadly toxin encoding genes."

Jacobo Reyes-Velasco, a
graduate student from Castoe's lab, is lead author on the new paper. In
addition to Castoe and Mackessy, other co-authors are: Daren Card, Audra
Andrew, Kyle Shaney, Richard Adams and Drew Schield, all from the UT Arlington
Department of Biology; and Nicholas Casewell, of the Liverpool School of
Tropical Medicine.

The paper is titled
"Expression of Venom Gene Homologs in Diverse Python Tissues Suggests a
New Model for the Evolution of Snake Venom." The abstract is available online at:

The research team
looked at 24 gene families that are shared by pythons, cobras, rattlesnakes and
Gila monsters, and associated with venom. The traditional view of venom
evolution has been that a core venom system developed at one point in the
evolution of snakes and lizards, referred to as the Toxicofera, and that the
evolution of highly venomous snakes, known as caenophidian snakes, came
afterward. But little explanation has been given for why evolution picked just
24 genes to make into highly toxic venom-encoding genes, from the 25,000 or so
possible.

"We believe that
this work will provide an important baseline for future studies by venom
researchers to better understand the processes that resulted in the mixture of
toxic molecules that we observe in venom, and to define which molecules are of
greatest importance for killing prey and causing pathology in human snakebite
victims," Casewell said.

When they looked at the
python, the team found several common characteristics among the venom-related
gene families that differed from other genes. Compared with other python gene
families, venom gene families are "expressed at lower levels overall,
expressed at moderate-high levels in fewer tissues and show among the highest
variation in expression level across tissues," Castoe said.

"Evolution seems to
have chosen what genes to evolve into venoms based on where they were expressed
(or turned on), and at what levels they were expressed," Castoe said.

Based on their data,
the new paper presents a model with three steps for venom evolution. First,
these potentially venomous genes end up in the oral gland by default, because
they are expressed in low but consistent ways throughout the body. Then,
because of natural selection on this expression in the oral gland being
beneficial, tissues in the mouth begin expressing those genes in higher levels
than in other parts of the body. Finally, as the venom evolves to become more
toxic, the expression of those genes in other organs is decreased to limit
potentially harmful effects of secreting such toxins in other body tissues.

The team calls its new
model the Stepwise Intermediate Nearly Neutral Evolutionary Recruitment, or
SINNER, model. They say differing venom levels in snakes and other animals
could be traced to the variability of where different species, or different
genes within a species, are along the continuum between the beginning and end
of the SINNER model.

Castoe said the next step
in the research would be to examine the genome of highly venomous snakes
to see if the SINNER model bears out. For now, he and the rest of the team hope
that their findings about the presence of venom-related genes in other parts of
the python change some thinking on what species are labeled as venomous.

"What is a venom
and what species are venomous will take a lot more evidence to convince people
now," Castoe said. "It provides a brand new perspective on what we
should think of when we look at those oral glands."

Thursday, December 4, 2014

The
Valle de Aguán spiny-tailed iguana is a critically endangered species found in
Honduras. A recent survey of people living in the region shows that, although
residents are aware of the endangered status of the species, the iguana
continues to be hunted for food. Of particular concern is the preference for
the consumption of female iguanas that are gravid (carrying eggs in their
body).

"In
this study we worked to gain a better understanding of how humans are
harvesting the species for food," said Stesha Pasachnik, Ph.D., a lead
researcher on the study and a postdoctoral research associate for the San Diego
Zoo Institute for Conservation Research. "The information we gained
indicates a use that is not only not sustainable but is likely to accelerate
this species' extinction due to the loss of gravid females."

Published
in the December issue of Herpetological Conservation and Biology, the
study gained firsthand information regarding the hunting, harvesting and
consumption of the species. Although the study, supported by the Bay Islands
Foundation and San Diego Zoo Global, highlights an area of serious concern, it
also recommends work to educate residents about the species and ways that
harvesting can be made more sustainable.

Bringing
species back from the brink of extinction is the mission of San Diego Zoo
Global. As a leader in conservation, the work of San Diego Zoo Global includes
onsite wildlife conservation efforts (representing both plants and animals) at
the San Diego Zoo, San Diego Zoo Safari Park, and San Diego Zoo Institute for
Conservation Research, as well as international field programs on six
continents. The important conservation and science work of these entities is
made possible by the San Diego Zoo Wildlife Conservancy and is supported in
part by the Foundation of the Zoological Society of San Diego.

Thursday, November 27, 2014

The question of what are turtles has been a source of a lively scientific debate over the past decades. Until recently, the phylogenetic placement of turtles within Amniota was uncertain and controversial. Molecular studies at the genome level confirm their sister relationship to archosaurs and rejected their relationship to lepidosaurs. However, relationships of lineages of turtles have not been studied using genomic techniques.

In a forthcoming paper in Molecular Phylogenetics and Evolution Crawford and colleagues (in press 2014) provide the first genome-scale analysis of turtle phylogeny. They sequenced 2381 ultraconserved element (UCE) loci representing a total of 1,718,154 bp of aligned sequence. The sampling includes 32 turtle taxa representing all 14 recognized turtle families and six additional outgroups.

This robust phylogeny shows that proposed phylogenetic names correspond to well-supported clades, and this topology is more consistent with the temporal appearance of clades and paleobiogeography.

The ultraconserved element (UCE) loci phylogeny supports the monophyly of Cryptodira, with Trionychia as the sister taxon to all other cryptodires. The clade including non-trionychian cryptodires was previously phylogenetically defined as ‘Durocryptodira’ by Danilov and Parham. The topology from ultraconserved elements and other molecular studies support the monophyly and the recognition of Durocryptodira, which is in contrast with the morphological hypothesis.

Combining the UCE phylogeny with the known fossil record of turtles allows reconstruction of some global biogeographic patterns. Intercontinental dispersal of turtles is common, usually involving a limited number of species.

The earliest fossils of stem testudinoids, stem trionychians, and stem cryptodires are from Eurasia. Mapping this onto the UCE phylogeny suggests cryptodires originated in the Jurassic of Eurasian. The emergence of cryptodires in Eurasia is complemented by the concurrent origin of pan-pleurodires in the Southern Hemisphere (Gondwana). Given the distribution of the clades and the timing of their origin, the geography of the cryptodire-pleurodire split can be plausibly linked to the breakup of the supercontinent Pangaea; a pattern common to other terrestrial vertebrates (e.g., placental vs. marsupial mammals).

Despite the Jurrasic
origin of cryptodiran turtles they did not dominate the fauna of northern
continents for 100 million years (in the Cenozoic). Instead, stem turtles
mostly the Paracryptodira) were diverse and abundant in North America during
the Cretaceous and into the Cenozoic. In the late Cretaceous cryptodires
started to appear in North America invading via high latitude dispersal routes.
The UCE phylogeny confirms one of the North American durocryptodire lineages,
the Americhelydia, underwent a modest radiation and accounts for 38 living
species.

Warm periods in the
Paleogene are responsible for the dispersal of many organinsism into North
America through high latitude dispersal routes, including a wave of
testudinoids. Two are modest radiations, four species of Gopherus (Testudinidae); nine
species of Rhinoclemmys (Geoemydidae).
Previous studies suggested that these genera are sister taxa to all of the Old
World members of their respective clades. The authors sequenced Gopherus, Rhinoclemmys, and representative divergent members of geoemydids
and testudinids and confirm the basal position of these North American genera.
This pattern links the overall diversification at the base of these clades with
their intercontinental dispersal, which can logically be attributed to periods
of warm climate.

Similar to the
Americhelydia, short branches within the testudinoids also suggest a rapid
adaptive radiation that coincides with high latitude intercontinental dispersal
events. This pattern suggests that global climate change has a major impact on
the diversity and distribution of turtles.

The end of the
Paleogene (∼45–23 Ma)
coincides with global environmental changes, with the climate becoming significantly
cooler and drier, thus much less favorable to turtles. Many turtle lineages
that inhabited the Western Interior, including the last stem cryptodires in
North America, became extinct at this time. One testudinoid lineage took
advantage of the subtropical southeastern portions of the continent and radiated
into the diverse clade Emydidae (53 species).

The recent
description of a fossil taxon on the stem of Platysternon megacephalum from the Eocene of North America
raises possibility that the more inclusive Emysternia may also have an American
origin. Depending on the resolution of that possibility, the UCE topology
indicates that two dispersal events into North America led to the origin of
36–43% of the recognized families of turtles.

Saturday, November 22, 2014

Conservation of sea snakes is virtually nonexistent in
Asia, and its role in human–snake interactions in terms of catch, trade, and
snakebites as an occupational hazard is mostly unexplored. In a recent paper in
Biological Conservation Nyguen et al
(2014) report data on sea snake landings from the Gulf of Thailand, a hotspot
for sea snake harvest by squid fishers operating out of the ports of Song Doc
and Khanh Hoi, Ca Mau Province, Vietnam. The information was collected during
documentation of the steps of the trading process and through interviewers with
participants in the trade. Squid vessels return to their ports once per lunar
synodic cycle and fishers sell snakes to merchants who sort, package, and ship
the snakes to various destinations in Vietnam and China for human consumption.
They are also used as a source of traditional remedies. Annually, 82 tons, roughly
equal to 225,500 individual snakes, of live sea snakes are brought to ports. Knowledge
of the harvest has been largely ignored and the rate of harvest constitutes one
of the largest venomous snake and marine reptile harvest activities in the
world today. In the harvest two species, Lapemis
curtus and Hydrophis cyanocinctus,
constituted about 85% of the snake biomass, and Acalyptophis peronii, Aipysurus
eydouxii, Hydrophis atriceps, H. belcheri, H. lamberti, and H. ornatus
made up the remainder. The results of this new paper establish a quantitative
baseline for characteristics of catch, trade, and uses of sea snakes. Other key
observations include the timing of the trade to the lunar cycle, a decline of
sea snakes harvested over the study period (approximately 30% decline in mass
over 4 years), and the treatment of sea snake bites with rhinoceros horn.
Emerging markets in Southeast Asia drive the harvest of venomous sea snakes in
the Gulf of Thailand and sea snake bites present a potentially lethal
occupational hazard.

The authors suggest that the Gulf of Thailand/southern
Vietnam is one of the largest harvests of venomous snake and marine reptiles in
the world. Yet sea snakes are not even mentioned in studies concerning reptile exploitation
in Asia or globally. This underreported status is particularly notable given
that the Indonesian archipelago has the highest marine species diversity in
general and specifically is among the areas ranked as having the greatest
richness of sea snake species on Earth. Still, in this area an unexplained decline
of sea snakes has been reported. The eight commercially traded sea snake
species reported on represent a significant proportion of the 20 species known
in the Gulf of Thailand and of the 25 species known from Vietnam, including the
South China Sea.

Globally, 9% of sea snakes are threatened, 6% are near
threatened, and 34% are data deficient, as defined by the International Union
for the Conservation of Nature (IUCN). The species in this study, as well as
all other species known from the Gulf of Thailand, are currently categorized as
either least concern or data deficient. However, the results suggest that in
the Gulf of Thailand a large subset of the sea snake species now considered as least
concern or data deficient may, in fact, be in danger of having their
populations damaged or destroyed through over harvesting. According to the results
presented in this paper, the number of sea snakes harvested from the Gulf of
Thailand by boats based at the study sites was 6.35 specimens per square kilometer per year. The
authors could not exclude the possibility that sea snake species in addition to
those observed were traded from other harvesting grounds (e.g., harvest landing
in Vung Tau, Vietnam). The volume of harvested sea snakes
documented is a conservative estimate of the total harvest from the Gulf of
Thailand. It is very likely that more snakes were harvested by squid vessels
and trawlers that originated from ports in Malaysia and Thailand. Sea snakes
have been brought into the ports of Songkhla, Thailand, Kra Isthmus, Thailand, and
Endau, Malaysia. Sea snake harvests similar to the one reported here could be
occurring in (or spread to) other areas of the South China Sea and wider
Southeast Asia. Ten years ago in Quảng Ng˜ai, the sea snake bycatch was
discarded due to fear of bites and a lack of market; however, in 2011 their
price was US$10–35/kg. Knowledge of the biology of sea snakes and their role in
the ecosystem is limited. Thus, understanding of the effect that this harvest may
have on populations or on the wider ecosystem is limited. The results supply
evidence that the mass of snakes harvested from the Gulf of Thailand has been
decreasing since 2009, and fishers interviewed consistently reported a decline
since they first began capturing sea snakes as a commodity.

Snake bites during the trade process are occupational hazards
that carry a high risk given the lethal venoms and lack of availability of
antivenin therapy. The economic incentive of harvesting sea snakes, from the
fishers’ and merchants’ perspectives, clearly outweighs the snake bite risk.
With respect to fatalities the authors report, one affected family continued trading
in sea snakes, while another family terminated participation in the snake
trade.

The authenticity and effectiveness of rhinoceros horn
and other locally used remedies for snake bites remains unproven. Yet, use of
rhinoceros body parts in Vietnam has been directly linked to poaching of
rhinoceros in South Africa. The observation suggests a link between rhinoceros
poaching and sea snake harvest in the Gulf of Thailand. Both fishers and merchants take advantage of
emerging market opportunities. According to the merchants, government, and
nongovernmental officials interviewed, the large-scale harvest of sea snakes from
the Gulf of Thailand is tied to economic prosperity and thus increase demand
domestically in Vietnam and from China for snake products. The demand is due to
the perceived health benefits of sea snakes and consumption of sea snakes as
status

Items. This particular sea snake harvest has been
going on essentially unnoticed by national and international conservation organizations
for more than a decade, in part because it apparently does not overtly conflict
with Vietnamese laws. Yet, given the volume of snakes and the wide spectrum of
species extracted and that the environmental effects of the harvest are
unknown, immediate attention by conservation organizations to sea snake
harvesting appears warranted. Ironically, the enforcement of laws aimed at
managing the trade in widely harvested terrestrial snakes, such as various
cobra species (e.g., Naja spp., Ophiophagus hannah), may have the
unintended consequence of increasing the market for sea snakes.

Monday, November 17, 2014

The Neotropical colubrid genus Chironius contains a monophyletic assemblage of snakes having very
low (10 or 12) dorsal scale rows at midbody. Currently the genus includes 20
species of diurnal snakes distributed from Honduras south to Uruguay and
northeastern Argentina. Recently, a lectotype was designated for Chironius flavolineatus, a widespread
species in open formations of South America (particularly in the Cerrado and
Caatinga), with records from Marajó island, northern Brazil. Chironius flavolineatus is distinguishable
from other members of the genus by the presence of a conspicuous yellow
vertebral stripe bordered anteriorly by black. In a new Zootaxa paper, Fernandes
and Hamdan (2014) describe the 21st species of Chironius, C.diamantine which differs from other Chironius in the combination of its
color pattern, 2-4 temporal scales, an entire anal plate, 6-10 rows of dorsal
scales at midbody, and some other characters. The new species is known from
municipalities of Morro do Chapéu, Rio de Contas, and Palmeiras in the Chapada
Diamantina, Bahia, Brazil. All specimens were found between sea level
1000 m asl. One individual was observed foraging about 3:00 PM on the banks of
a rocky river near a waterfall, a few minutes later plunged into the river and
remained there for about two minutes.

Citation

Fernandes
DS, & Hamdan B. 2014. A new species of Chironius
Fitzinger, 1826 from the state of Bahia, Northeastern Brazil (Serpentes:
Colubridae). Zootaxa, 3881(6), 563-575.

Sunday, November 16, 2014

The Old World Rat Snakes have been a source of
confusion for many years, they have a diverse morphology and behaviors that
have been a puzzle to herpetologists for some time - the kind of puzzle best
solved with molecular techniques. The last decade has seen an incredible rise
in the use of molecular phylogenies to examine relationships in snakes, assess
biogeographic origins, understand processes of adaptive radiation and
ultimately correct taxonomy with regard to paraphyletic and polyphyletic groups
at multiple levels. The importance of using phylogenetic trees to uncover
genealogical relationships and properly construct a taxonomy of organisms
cannot be overstated. The development of DNA sequencing technology has
increased the available genetic data for phylogenetic inference and the
development of model-based statistical methods, such as maximum likelihood and
Bayesian inference, which has enhanced the reliability of reconstructed
phylogenies. Using molecular data to examine phylogenetic relationships
provides evidence to clarify systematic ambiguities from morphological
characters and helps avoid misleading relationships due to convergence of
morphology. Therefore, an abundance of molecular data with information from
independent loci is able to provide strong evidence to assess taxonomic
composition and test monophyly.

Using one mitochondrial gene and five nuclear loci, Xin
Chen and colleagues (2014) evaluated the taxonomic status of a rare Borneo
endemic, the Rainbow Tree Snake Gonyophis
margaritatus. The authors inferred a molecular phylogeny of 101 snake
species. Both maximum likelihood and time- calibrated Bayesian inference
phylogenies demonstrated that G.
margaritatus is sister to the Green Trinket Snake, Rhadinophis prasinus of northern Thailand, previously considered to
be part of a radiation of Old World ratsnakes. This group is in turn sister to
a group containing Rhadinophis frenatus
(India, southern China, Taiwan, and North Vietnam) and the Rhinoceros Ratsnake, Rhynchophis
boulengeri with the entire clade originating in the mid-Miocene (~16 Ma) in
Southeast Asia. This group is sister to the genus Gonyosoma and together originated in the early Miocene (~20 Ma). The
authors discuss three potential solutions towards eliminating polyphyly of the
genus Rhadinophis, but recommend
using the genus name Gonyosoma for
all species within this clade, which currently contains all of the species
within the genera Gonyosoma, Gonyophis, Rhadinophis, and Rhynchophis.

Through
the careful study of modern and early fossil tortoise, researchers now have a
better understanding of how tortoises breathe and the evolutionary processes
that helped shape their unique breathing apparatus and tortoise shell. The
findings published in a paper, titled: Origin of the unique ventilatory
apparatus of turtles, in the scientific journal, Nature Communications, on
Friday, 7 November 2014, help determine when and how the unique breathing
apparatus of tortoises evolved.

Lead
author Dr Tyler Lyson of Wits University's Evolutionary Studies Institute, the
Smithsonian Institution and the Denver Museum of Nature and Science said:
"Tortoises have a bizarre body plan and one of the more puzzling aspects
to this body plan is the fact that tortoises have locked their ribs up into the
iconic tortoise shell. No other animal does this and the likely reason is that
ribs play such an important role in breathing in most animals including
mammals, birds, crocodilians, and lizards."

Instead
tortoises have developed a unique abdominal muscular sling that wraps around
their lungs and organs to help them breathe. When and how this mechanism
evolved has been unknown.

"It
seemed pretty clear that the tortoise shell and breathing mechanism evolved in
tandem, but which happened first? It's a bit of the chicken or the egg
causality dilemma," Lyson said. By studying the anatomy and thin sections
(also known as histology), Lyson and his colleagues have shown that the modern
tortoise breathing apparatus was already in place in the earliest fossil
tortoise, an animal known as Eunotosaurus
africanus.

This
animal lived in South Africa 260 million years ago and shares many unique
features with modern day tortoises, but lacked a shell. A recognizable tortoise
shell does not appear for another 50 million years.

Lyson
said Eunotosaurus bridges
the morphological gap between the early reptile body plan and the highly
modified body plan of living tortoises, making it the Archaeopteryx of turtles.

"Named
in 1892, Eunotosaurus is
one of the earliest tortoise ancestors and is known from early rocks near
Beaufort West," said Professor Bruce Rubidge, Director of the Evolutionary
Studies Institute at Wits University and co-author of the paper.

"There
are some 50 specimen of Eunotosaurus.
The rocks of the Karoo are remarkable in the diversity of fossils of early
tortoises they have produced. The fact that we find Eunotosaurus at the base of the Karoo succession strongly
suggest that there are more ancestral forms of tortoises still to be discovered
in the Karoo," Rubidge added.

The
study suggests that early in the evolution of the tortoise body plan a gradual
increase in body wall rigidity produced a division of function between the ribs
and abdominal respiratory muscles. As the ribs broadened and stiffened the
torso, they became less effective for breathing which caused the abdominal
muscles to become specialized for breathing, which in turn freed up the ribs to
eventually -- approximately 50 million years later -- to become fully
integrated into the characteristic tortoise shell.

Lyson
and his colleagues now plan to investigate reasons why the ribs of early
tortoises starting to broaden in the first place. "Broadened ribs are the
first step in the general increase in body wall rigidity of early basal
tortoises, which ultimately leads to both the evolution of the tortoise shell
and this unique way of breathing. We plan to study this key aspect to get a
better understanding why the ribs started to broaden."

Thursday, November 6, 2014

When
it comes to genitalia, nature enjoys variety. Snakes and lizards have two.
Birds and people have one. And while the former group's paired structures are
located somewhat at the level of the limbs, ours, and the birds', appear a bit
further down. In fact, snake and lizard genitalia are derived from tissue that
gives rise to hind legs, while mammalian genitalia are derived from the tail
bud. But despite such noteworthy contrasts, these structures are functionally
analogous and express similar genes.

How
do these equivalent structures arise from different starting tissues?

This
is a python embryo at 11 days after

oviposition (egglaying). The right
hemipenis

(genitalia) bud and vestigial limb-bud can be

seen near the tail end
of the embryo, in the

center of the tail 'spiral'. (two white 'blobs').

Photo Credit: Patrick
Tschopp.

Reporting
in Nature, researchers in Harvard Medical School's Department of Genetics, led
by departmental chair Clifford Tabin, have found that the answer is not unlike
the real estate axiom Location, location, location.

The
embryonic cloaca -- which eventually develops into the urinary and gut tracts
-- issues molecular signals that tell neighboring cells and tissues to form
into external genitalia. The cloaca's location determines which tissues receive
the signal first. In snakes and lizards, the cloaca is located closer to the
lateral plate mesoderm, the same tissue that makes the paired limbs, receives
the signal. In mammals, the cloaca is closer to the tail bud.

To
further confirm this finding, the researchers grafted cloaca tissue next to the
limb buds in one group of chicken embryos, and beside the tail buds in a second
group. They found that in both cases, cells closer to the grafted cloaca
responded to the signals and partially converted toward a genitalia fate.

This
proves that different populations of cells with progenitor potential are able
to respond to cloaca signaling and contribute to genitalia outgrowth.

"While
mammal and reptile genitalia are not homologous in that they are derived from
different tissue, they do share a 'deep homology' in that they are derived from
the same genetic program and induced by the same ancestral set of molecular
signals," said Tabin, who is also the George Jacob and Jacqueline Hazel
Leder Professor of Genetics.

"Here
we see that an evolutionary shift in the source of a signal can result in a
situation where functionally analogous structures are carved out of
nonhomologous substrate," said Patrick Tschopp, an HMS research fellow in
genetics in Tabin's lab and first author on the paper. "Moreover, this
might help to explain why limbs and genitalia use such similar gene regulatory
programs during development."

Fossil
remains show the first amphibious ichthyosaur found in China by a team led by a
UC

Davis scientist. Its amphibious characteristics include large flippers and
flexible wrists, essential

for crawling on the ground. Photo Credit: Ryosuke
Motani/UC Davis

The
first fossil of an amphibious ichthyosaur has been discovered in China by a
team led by researchers at the University of California, Davis. The discovery
is the first to link the dolphin-like ichthyosaur to its terrestrial ancestors,
filling a gap in the fossil record. The fossil is described in a paper
published in advance online Nov. 5 in the journal Nature.

The
fossil represents a missing stage in the evolution of ichthyosaurs, marine
reptiles from the Age of Dinosaurs about 250 million years ago. Until now,
there were no fossils marking their transition from land to sea.

"But
now we have this fossil showing the transition," said lead author Ryosuke
Motani, a professor in the UC Davis Department of Earth and Planetary Sciences.
"There's nothing that prevents it from coming onto land."

Motani
and his colleagues discovered the fossil in China's Anhui Province. About 248
million years old, it is from the Triassic period and measures roughly 1.5 feet
long.

Unlike
ichthyosaurs fully adapted to life at sea, this one had unusually large,
flexible flippers that likely allowed for seal-like movement on land. It had
flexible wrists, which are essential for crawling on the ground. Most
ichthyosaurs have long, beak-like snouts, but the amphibious fossil shows a
nose as short as that of land reptiles.

Its
body also contains thicker bones than previously-described ichthyosaurs. This
is in keeping with the idea that most marine reptiles who transitioned from
land first became heavier, for example with thicker bones, in order to swim
through rough coastal waves before entering the deep sea.

The
study's implications go beyond evolutionary theory, Motani said. This animal
lived about 4 million years after the worst mass extinction in Earth's history,
252 million years ago. Scientists have wondered how long it took for animals
and plants to recover after such destruction, particularly since the extinction
was associated with global warming.

"This
was analogous to what might happen if the world gets warmer and warmer,"
Motani said. "How long did it take before the globe was good enough for
predators like this to reappear? In that world, many things became extinct, but
it started something new. These reptiles came out during this recovery."

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